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In veterinary medicine, large quantities of antibiotic substances are administered each year for therapeutic and prophylactic purposes or to promote growth. As a consequence, the antibiotics and bacteria carrying transferable antibiotic resistance genes are excreted by the animals and reach the environment through run-off, leaching, and/or following manure application to agricultural fields, where they have been found to affect the structure and function of soil bacterial communities. However, we are only beginning to understand the global effects of environmental pollution with antibiotics and resistance determinants and the resulting risks for human health. For regulatory purposes, there is urgent need for criteria and methods that allow reliable and reproducible assessment of risks associated with release of realistic concentrations of antibiotics and resistance determinants into the environment following manure application. In this chapter, we will summarize recent advances, limitations, and research needed to optimize the methods to quantify and evaluate the effects and risks associated with these compounds. Approaches that are discussed focus on antibiotic resistance genes and include classical tools such as cultivation and PCR detection as well as quantitative real-time PCR and next-generation sequencing technologies used in combination with functional screening.

Approaches to Assess the Effects and Risks of Veterinary Antibiotics Applied with Manure to Soil